2J2F

The T199D Mutant of Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Single Mutation in the Castor {Delta}9-18:0- Desaturase Changes Reaction Partitioning from Desaturation to Oxidase Chemistry.

Guy, J.E.Abreu, I.A.Moche, M.Lindqvist, Y.Whittle, E.Shanklin, J.

(2006) Proc Natl Acad Sci U S A 103: 17220

  • DOI: 10.1073/pnas.0607165103
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Sequence analysis of the diiron cluster-containing soluble desaturases suggests they are unrelated to other diiron enzymes; however, structural alignment of the core four-helix bundle of desaturases to other diiron enzymes reveals a conserved iron binding motif with similar spacing in all enzymes of this structural class, implying a common evolutionary ancestry ...

    Sequence analysis of the diiron cluster-containing soluble desaturases suggests they are unrelated to other diiron enzymes; however, structural alignment of the core four-helix bundle of desaturases to other diiron enzymes reveals a conserved iron binding motif with similar spacing in all enzymes of this structural class, implying a common evolutionary ancestry. Detailed structural comparison of the castor desaturase with that of a peroxidase, rubrerythrin, shows remarkable conservation of both identity and geometry of residues surrounding the diiron center, with the exception of residue 199. Position 199 is occupied by a threonine in the castor desaturase, but the equivalent position in rubrerythrin contains a glutamic acid. We previously hypothesized that a carboxylate in this location facilitates oxidase chemistry in rubrerythrin by the close apposition of a residue capable of facilitating proton transfer to the activated oxygen (in a hydrophobic cavity adjacent to the diiron center based on the crystal structure of the oxygen-binding mimic azide). Here we report that desaturase mutant T199D binds substrate but its desaturase activity decreases by approximately 2 x 10(3)-fold. However, it shows a >31-fold increase in peroxide-dependent oxidase activity with respect to WT desaturase, as monitored by single-turnover stopped-flow spectrometry. A 2.65-A crystal structure of T199D reveals active-site geometry remarkably similar to that of rubrerythrin, consistent with its enhanced function as an oxidase enzyme. That a single amino acid substitution can switch reactivity from desaturation to oxidation provides experimental support for the hypothesis that the desaturase evolved from an ancestral oxidase enzyme.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Division of Molecular Structural Biology, Karolinska Institutet, Tomtebodavägen 6, S-171 77 Stockholm, Sweden.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACYL-[ACYL-CARRIER-PROTEIN] DESATURASEA, B, C, D, E, F363Ricinus communisMutation(s): 1 
EC: 1.14.99.6 (PDB Primary Data), 1.14.19.2 (UniProt)
Find proteins for P22337 (Ricinus communis)
Explore P22337 
Go to UniProtKB:  P22337
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download CCD File 
A, B, C, D, E, F
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.049α = 90
b = 145.768β = 90
c = 193.245γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance